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Protein

Alpha-galacturonidase

Gene

lplD

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Alpha-galacturonidase able to catalyze the hydrolysis of the chromogenic substrate p-nitrophenyl-alpha-D-galacturonic acid (pNPalphaGalUA), and of the probable natural substrate alpha-1,4-di-galacturonate (GalUA2). Can neither hydrolyze pNPbetaGalUA, nor the stereoisomeric pNPalphaGlcUA. Does not display alpha- or beta-glucosidase activity as it fails to hydrolyze melibiose, raffinose, lactose and the chromogenic analogs, pNPalphaGal and pNPbetaGal. Cannot use the following compounds as substrates: pNP-N-acetyl-alpha- and beta-D-galactosaminide, pNP-N-acetyl-alpha- and beta-D-glucosaminide, pNP-alpha-L- and beta-L-arabinopyranoside, pNP-alpha- and beta-D-glucuronide, pNP-alpha- and beta-D-glucopyranoside, pNP-alpha- and beta-D-glucopyranoside 6-phosphate, pNP-alpha-D-galactopyranoside 6-phosphate and oNP-beta-D-galactopyranoside 6-phosphate.1 Publication

Catalytic activityi

((1->4)-alpha-D-galacturonide)(n) + H2O = ((1->4)-alpha-D-galacturonide)(n-1) + D-galacturonate.1 Publication

Cofactori

Protein has several cofactor binding sites:
  • NAD+1 Publication
  • Mn2+1 PublicationNote: Binds 1 Mn2+ ion per subunit. Although a Mg2+ ion is seen in the structure, galacturonidase activity was shown using manganese (PubMed:23416295).1 Publication

Kineticsi

kcat is 3.6 sec(-1) with pNPalphaGalUA as substrate (at about 37 degrees Celsius).

  1. KM=0.62 µM for pNPalphaGalUA (at about 37 degrees Celsius)1 Publication
  1. Vmax=4.33 µmol/min/mg enzyme with pNPalphaGalUA as substrate (at about 37 degrees Celsius)1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei151SubstrateBy similarity1
Metal bindingi173Manganese1
Active sitei174Proton donorBy similarity1
Metal bindingi210Manganese1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi10 – 72NADBy similarityAdd BLAST63

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase

Keywords - Biological processi

Carbohydrate metabolism

Keywords - Ligandi

Manganese, Metal-binding, NAD

Enzyme and pathway databases

BioCyciBSUB:BSU07130-MONOMER.

Protein family/group databases

CAZyiGH4. Glycoside Hydrolase Family 4.

Names & Taxonomyi

Protein namesi
Recommended name:
Alpha-galacturonidase (EC:3.2.1.67)
Gene namesi
Name:lplD
Ordered Locus Names:BSU07130
OrganismiBacillus subtilis (strain 168)
Taxonomic identifieri224308 [NCBI]
Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
Proteomesi
  • UP000001570 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi172C → L: Does not significantly affect alpha-galacturonidase activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001698621 – 446Alpha-galacturonidaseAdd BLAST446

Proteomic databases

PaxDbiP39130.

Interactioni

Subunit structurei

Homotetramer.2 Publications

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100004003.

Structurei

Secondary structure

1446
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi10 – 15Combined sources6
Turni16 – 18Combined sources3
Helixi22 – 32Combined sources11
Beta strandi38 – 43Combined sources6
Helixi47 – 57Combined sources11
Beta strandi65 – 69Combined sources5
Helixi73 – 77Combined sources5
Beta strandi81 – 85Combined sources5
Helixi92 – 100Combined sources9
Helixi101 – 105Combined sources5
Beta strandi113 – 115Combined sources3
Helixi116 – 140Combined sources25
Beta strandi144 – 148Combined sources5
Helixi153 – 163Combined sources11
Beta strandi168 – 171Combined sources4
Helixi175 – 191Combined sources17
Helixi198 – 200Combined sources3
Beta strandi201 – 208Combined sources8
Beta strandi211 – 219Combined sources9
Helixi224 – 235Combined sources12
Turni236 – 238Combined sources3
Helixi257 – 266Combined sources10
Beta strandi267 – 270Combined sources4
Helixi274 – 277Combined sources4
Helixi285 – 287Combined sources3
Turni289 – 293Combined sources5
Helixi299 – 318Combined sources20
Helixi332 – 339Combined sources8
Beta strandi345 – 352Combined sources8
Beta strandi354 – 357Combined sources4
Beta strandi364 – 373Combined sources10
Beta strandi376 – 380Combined sources5
Helixi387 – 409Combined sources23
Helixi412 – 421Combined sources10
Helixi429 – 439Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3FEFX-ray2.20A/B/C/D7-446[»]
ProteinModelPortaliP39130.
SMRiP39130.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP39130.

Family & Domainsi

Sequence similaritiesi

Belongs to the glycosyl hydrolase 4 family.Curated

Phylogenomic databases

eggNOGiENOG4105F8D. Bacteria.
COG1486. LUCA.
HOGENOMiHOG000270081.
InParanoidiP39130.
OMAiETANTME.
PhylomeDBiP39130.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
3.90.110.10. 1 hit.
InterProiIPR019802. GlycHydrolase_4_CS.
IPR001088. Glyco_hydro_4.
IPR022616. Glyco_hydro_4_C.
IPR015955. Lactate_DH/Glyco_Ohase_4_C.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF02056. Glyco_hydro_4. 1 hit.
PF11975. Glyco_hydro_4C. 1 hit.
[Graphical view]
PRINTSiPR00732. GLHYDRLASE4.
SUPFAMiSSF51735. SSF51735. 1 hit.
SSF56327. SSF56327. 1 hit.
PROSITEiPS01324. GLYCOSYL_HYDROL_F4. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P39130-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MFHISTLDQI KIAYIGGGSQ GWARSLMSDL SIDERMSGTV ALYDLDFEAA
60 70 80 90 100
QKNEVIGNHS GNGRWRYEAV STLKKALSAA DIVIISILPG SLDDMEVDVH
110 120 130 140 150
LPERCGIYQS VGDTVGPGGI IRGLRAVPIF AEIARAIRDY APESWVINYT
160 170 180 190 200
NPMSVCTRVL YKVFPGIKAI GCCHEVFGTQ KLLAEMVTER LGIEVPRRED
210 220 230 240 250
IRVNVLGINH FTWITKASYR HIDLLPIFRE FSAHYGESGY ELEGECWRDS
260 270 280 290 300
VFCSAHRVAF DLFETYGAIP AAGDRHLAEF LPGPYLKQPE VWKFHLTPIS
310 320 330 340 350
FRKQDRAEKR QETERLIVQQ RGVAEKASGE EGVNIIAALL GLGELVTNVN
360 370 380 390 400
MPNQGQVLNL PIQAIVETNA FITRNRVQPI LSGALPKGVE MLAARHISNQ
410 420 430 440
EAVADAGLTK DTGLAFQAFL NDPLVQIDRS DAEQLFNDML QCIMQS
Length:446
Mass (Da):49,487
Last modified:December 15, 1998 - v2
Checksum:i691FEC5C371B9F5B
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti66R → T in AAA22577 (Ref. 1) Curated1
Sequence conflicti154S → Y in AAA22577 (Ref. 1) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L19165 Genomic DNA. Translation: AAA22577.1.
AL009126 Genomic DNA. Translation: CAB12532.1.
PIRiC69653.
RefSeqiNP_388594.1. NC_000964.3.
WP_003244472.1. NZ_JNCM01000032.1.

Genome annotation databases

EnsemblBacteriaiCAB12532; CAB12532; BSU07130.
GeneIDi938770.
KEGGibsu:BSU07130.
PATRICi18973074. VBIBacSub10457_0751.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L19165 Genomic DNA. Translation: AAA22577.1.
AL009126 Genomic DNA. Translation: CAB12532.1.
PIRiC69653.
RefSeqiNP_388594.1. NC_000964.3.
WP_003244472.1. NZ_JNCM01000032.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3FEFX-ray2.20A/B/C/D7-446[»]
ProteinModelPortaliP39130.
SMRiP39130.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224308.Bsubs1_010100004003.

Protein family/group databases

CAZyiGH4. Glycoside Hydrolase Family 4.

Proteomic databases

PaxDbiP39130.

Protocols and materials databases

DNASUi938770.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAB12532; CAB12532; BSU07130.
GeneIDi938770.
KEGGibsu:BSU07130.
PATRICi18973074. VBIBacSub10457_0751.

Phylogenomic databases

eggNOGiENOG4105F8D. Bacteria.
COG1486. LUCA.
HOGENOMiHOG000270081.
InParanoidiP39130.
OMAiETANTME.
PhylomeDBiP39130.

Enzyme and pathway databases

BioCyciBSUB:BSU07130-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP39130.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
3.90.110.10. 1 hit.
InterProiIPR019802. GlycHydrolase_4_CS.
IPR001088. Glyco_hydro_4.
IPR022616. Glyco_hydro_4_C.
IPR015955. Lactate_DH/Glyco_Ohase_4_C.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF02056. Glyco_hydro_4. 1 hit.
PF11975. Glyco_hydro_4C. 1 hit.
[Graphical view]
PRINTSiPR00732. GLHYDRLASE4.
SUPFAMiSSF51735. SSF51735. 1 hit.
SSF56327. SSF56327. 1 hit.
PROSITEiPS01324. GLYCOSYL_HYDROL_F4. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiLPLD_BACSU
AccessioniPrimary (citable) accession number: P39130
Secondary accession number(s): O31532
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: December 15, 1998
Last modified: November 2, 2016
This is version 118 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Bacillus subtilis
    Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
  2. Glycosyl hydrolases
    Classification of glycosyl hydrolase families and list of entries
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.